Habitat quality has great significance for regional ecological conservation and human welfare. In this study, we evaluated the spatial and temporal characteristics of land use and habitat quality in the temperate desert sub-region of Ordos Plateau using patch-generating land use simulation (PLUS) and integrated valuation of ecosystem services and trade-offs (InVEST) models. From 2000 to 2020, the areas of grassland, cropland, and unused land in the study area increased significantly; the areas of water bodies and woodland increased slightly; and the area of wasteland decreased significantly. Moreover, the habitat quality in the temperate desert subzone of the Ordos Plateau showed a trend of increasing and then decreasing from 2000 to 2020. The areas of lower and low habitat quality first decreased and then increased, and the overall area decreased over time. Conversely, the areas of high and higher habitat quality initially increased and then decreased, and the overall area increased over time. The area of medium habitat quality first decreased and then increased, although the overall change was minimal. Based on the PLUS model, the habitat quality of the study area in 2025 predicted under the natural development scenario was compared with that predicted under the ecological conservation scenario, showing higher habitat quality and lower habitat degradation under the ecological conservation development scenario. These results can be used to provide a scientific basis and decision reference for the sustainable use of land resources and high-quality socio-economic development in the temperate desert sub-region of the Ordos Plateau.